On Bonaire, there's sort of 3-4 distinct areas to stay at. Each one has it's advantages or disadvantages depending on what you're looking for. All of them are near/on the water but each is slightly different.
North of town you've got the dive resorts, Buddy's Capt. Don's, Harbour Village, Sanddollar and Lion's Dive - and others. These tend to be more all-inclusive and provide a lot of services for a slightly higher price. All of them are on one of Bonaire's many good reefs so they all offer shorediving at their facilities. You can stay there, eat meals there, dive with them and never leave the area. It's a short drive to downtown or the Airport from this area. They all offer some convenient way to get tanks, Buddy's even has a drivethrough, so it's easy to shoredive from any of them if you rent a truck. Harbour Village is the most upscale followed by Lions Dive then the others. Buddy just bought Lion's Dive so they share the Buddy dive op now. Sanddollar is the most reasonable if you want to be on the water and it's right off Bari Reef.
A little to the northeast of town, and not exactly on the water there is another residential/condo area, places like Golden Reef Inn and Lagoen Hill are a couple of places that feature nice reasonable accommodations but not on the water. Golden Reef has to be one of the best deals in this area and fairly new.
Downtown there are less accommodations and more of the restaurants, fast food - there's a KFC on Bonaire - and local eateries are located there. There's a couple of smaller hotel/condo complexes north of the Town Pier area, but not a lot of diveops in the area except for a satellite Toucan shop at one of the smaller rental properties. There is a weeekly efficiency apartment rental complex in that area I've heard mentioned on Bonaire Talk as being reasonable and near everything and just across the street from the water but there's no shoredive sites in the Kralendijk area except for Town Pier and you can't dive it unless accompanied by a DM at night.
Further south of town are the Divi and Plaza resorts. Divi is a full service diveresort with their own reef and the only casino on island if that appeals to you. From there the reef kind of tapers off in front of Plaza, so although they teach there, most of their diving is done elsewhere, either via boat or shoredive. Plaza's a nice place and they're offering a special for SB members. Toucan Dive runs out of there, we dove with them last summer and are recommended.
Then a mile or so farther south of there, and past the airport is Belnem, it's probably the quietest area, with condo rentals both on-water and just off. We stay at BelMar condos in this area, but there are no nearby restaurants so everything is a 5 minute drive from there back to town.
The shoredive sites on Bonaire generally fall into sites south of Belnem and the Airport all the way down to the Salt Flats/Salt Pier and Lighthouse at the farthest south end - about 2-3 miles - or the northern sites which start just past the diveresorts and go all the way up into the Slagbaai Park. Both are equally good, the southern sites feature the Hooker wreck, the Salt Pier - which is DM-accompanied only now - as well as over a dozen more good sites, like Invisibles, Angel City etc, leading down to the more difficult(due to currents) sites like Red Slave and Lighthouse. The reef structure is flatter and most entries are off ironshore flat beaches. With a truck you can literally drive to within 20-30' of the water at all of them, suit up and make your entry. In a lot of cases, the truck also is your shore marker.
The northern sites are the classic Bonaire sites, Karpata, 1000 Steps, Rappel, Witches Hut etc. These are some of the best due to the structure of the reef but can be harder to get to in some cases, requiring a bit of a walk from the parking areas down to the shore, although some of them are drive-up near the water also. Rappel being the only exception, it's a boat dive only. There can be some trickier entries there, for example at La Dania's leap, you leap into the water and swim around and get out at Karpata, it's a one way trip.
If you're trying to save money, my suggestion would be find someplace affordable around town. Golden Reef would be high on my list, also Black Durgon Inn, Carib Inn or Eden Beach although it's a little farther out. Definitely rent a truck, go to Cultimara for groceries and drive to the inexpensive places to eat. There are 1/2 dozen affordable places in town, Zee Zicht, Donna & Giorgios, the bar/restaurant just north of Town Pier,(don't remember the name) the last day there we found a takeout barbeque place about 2 blocks north of downtown, it smelled so good we almost canceled our restaurant reservations.
As mentioned previously do single boat dives if desired, we paid $18 one afternoon to go to Forest off Klein with Toucan Dive. Do a couple of boat dives to Klein if you can afford it, it's different than the rest of Bonaire.
Have you priced airfare? that was the most expensive part for us. From Phoenix there's usually an overnight somewhere. I assume Denver's similar. We got around it by getting a cheap Southwest flight to LAX then flying the American Airlines red-eye to Puerto Rico, spent the day in PR then on to Bonaire in the later afternoon, it still took basically 26 hrs. to get there, we just didn't have to pay for a room somewhere by sleeping on the plane. Return flights were better we left BON at 8am and were back home by early evening.
PM if you have any other specific questions,
Steve
P.S. I agree with everything Herman says...
almtree::sunny 
the friendliest! 
don 
